Processes quantitative analyses of high throughput cell migration assay. WIS-PhagoTracker facilitates morphometric analysis of modified Phagokinetic tracks that are visualized by using a screening microscope. This software applies a multi-scale segmentation algorithm to characterize several morphometric parameters such track area, perimeter, major and minor axis and solidity for each track. It can support single image files and run batch processing of multiple plates.
A computational framework to annotate complex cellular dynamics. A machine-learning method that combines state-of-the-art classification with hidden Markov modeling for annotation of the progression through morphologically distinct biological states was developed. CellCognition is published as open source software, enabling live-cell imaging-based screening with assays that directly score cellular dynamics.
Analyzes, processes and visualizes multi-dimensional microscopy images. BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes.
Performs crowd-based images annotation. Quanti.us is a portal that assists users in recruiting groups of untrained Mechanical Turk workers (Turkers) to annotate images using a set of interaction tools. The platform enables uploading of image sets, selection of an analysis tool, and provides sets of instructions. Users can gather hand annotations by marshaling paid Turkers to annotate a range of image types. Quanti.us thus makes crowd analysis of scientific images applicable to several annotation problems.
A free, open-source system designed for flexible, high-throughput cell image analysis. CellProfiler can address a variety of biological questions quantitatively, including standard assays (for example, cell count, size, per-cell protein levels) and complex morphological assays (for example, cell/organelle shape or subcellular patterns of DNA or protein staining).
Finds dynamic changes in pixel intensity between image frames. MUSCLEMOTION expresses the output as a relative measure of movement during muscle contraction and relaxation. It can be employed for multiparameter recording conditions and experimental settings using transmitted light microscopy, fluorescent membrane labeling, fluorescent beads embedded in soft substrates or patch clamp video recordings.
Provides a platform dedicated to the correlation of biosensor activity with the velocity of neighboring regions of the cell edge. EdgeProps is a standalone software that investigates links several parameters such as signaling activity or protrusion persistence and that includes multiple representations of edge dynamics. The application ascertains activation level and velocity at each point over time for a series of points that are equally spaced throughout the edge.
Correlates local cortical fluorescence with membrane movement. Quimp is based on the electrostatic contour migration method (ECMM) that consists of an improvement of a boundary tracking approach. It reduces sum of path lengths connecting all pairs of points, equivalent to minimizing the energy required for cell deformation. This tool is useful to study time series of several hundreds of cells per experimental condition.
A tool for segmentation, fluorescence quantification, and tracking of cells on microscopy images. CellX decodes the information across the cell membrane and guarantees optimal detection of the cell boundaries on a per-cell basis. Graph cuts account for the information of the cell boundaries through directional cross-correlations, and they automatically incorporate spatial constraints. The method accurately segments images of various cell types grown in dense cultures that are acquired with different microscopy techniques.
A user-friendly opensource software tool for tracking cells imaged with various imaging modalities, including fluorescent, phase contrast, and differential interference contrast (DIC) techniques. The main goals of the software tool are: (i) automated image quality enhancement using vignetting and alignment correction, (ii) detection and tracking of cells, (iii) editing cell paths and statistical analysis of the cell motion.
Supplies a method for ranking cellular morphodynamics. SquigglyMorph is an application permitting the investigation and the displaying of regions of protrusion and retraction. It includes features that allows users to (i) build smoothed curves (ii) assess centroid speed and persistence and (iii) display cell boundary, distribution profile of protruding boundary points, rate of area change or polarization parameter as functions of time.
Allows analysis of epithelial tissues. EpiTools automates image analysis including cell segmentation and cell tracking. It describes dynamic cellular behavior and allows users to study the power of in vivo imaging. This tool supplies a graphical user interface to simplify its utilization by users and for segmenting and tracking the contours of cell membrane signals obtained from 4D confocal imaging. It is intended primarily for biologists with no computer-science background.
Analyzes and detects cell migration and morphodynamics. ADAPT permits rapid whole-cell analysis of time-lapse videos, providing data on cell morphology, membrane velocity, and temporal changes in any fluorescent protein of interest at the cell periphery. It allows the tracking of cell migration and the automated detection of individual membrane protrusions, outputting data on local membrane velocity, change in protrusion size, and local recruitment of proteins to the cell membrane.
Investigates cellular protrusion dynamics. CellGeo is a platform dedicated to cell protrusions tracking and other changes in morphology. It is built around: (i) an unsupervised mode that allows users to manage their data and to apply default or a recorded set of parameter values and; (ii) an exploratory mode to ease settings calibration by observing their effects directly on the analysis. It also includes five modules providing features for specific protrusions identification as well as for visualization or mapping.
Allows users to submit time-lapse fluorescence image sets of focal adhesion (FA) proteins and have these images automatically analyzed. FAAS provides a set of webpages for uploading a stacked TIFF set of images for processing. The processing pipeline is then run, and the results are returned as a downloadable zip file. The user is provided with two types of visualizations that show either the entire field of view or single adhesions over time. The software can extract and quantify a wide range of properties.
Provides general purpose functionality for reading, writing, processing and analysis of images. In the context of microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and use of existing tools in the R environment for signal processing, statistical modeling, machine learning and data visualization. It uses ImageMagick to read and save images, and supports more than 80 image formats, including JPEG, TIFF, TGA, GIF and PNG. EBImage also supports standard geometric transformations such as rotation, reflection, cropping, translation and resizing. Classical image processing tools are available: linear filtering, morphological erosion and dilation, fast distance map computation, contour delineation and area filling.